We have proteomics data from three different strains of T7 after 1, 5, and 9 minutes of infection in E. coli. Each time point has 2 replicates for a total of 18 samples.
evol: evolved phage with codon-modified gene 10
atten: initial codon-modified gene 10 phage
wt: wild-type phage
Normalization: Data are normalized by total protein area (T7 and E. coli) for each sample after computing areas or adjusting spectral counts with APEX.
Analyses by John Houser indicate that APEX-normalized spectral counts in E. coli corrlate more strongly with transcript levels than peak areas correlate with transcripts. These analyses examine APEX-normalized spectral counts for phage proteins.
Do we expect APEX to perform well with very highly expressed genes?
Averaged across all genes and all replicates for a given time point and given strain, class 3 protein levels look similar to gp10A (just barely). I have not actually tested to see if any strain is significantly different from another across all genes.
Above is a detailed breakdown of every class 3 gene. Several genes follow the same pattern as gp10A, but others do not.